DOI: 10.18129/B9.bioc.BgeeCall  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see BgeeCall.

Automatic RNA-Seq present/absent gene expression calls generation

Bioconductor version: 3.16

BgeeCall allows to generate present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee (

Author: Julien Wollbrett [aut, cre], Sara Fonseca Costa [aut], Julien Roux [aut], Marc Robinson Rechavi [ctb], Frederic Bastian [aut]

Maintainer: Julien Wollbrett <julien.wollbrett at>

Citation (from within R, enter citation("BgeeCall")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script automatic RNA-Seq present/absent gene expression calls generation
PDF   Reference Manual
Text   NEWS


biocViews GeneExpression, RNASeq, Software
Version 1.14.0
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License GPL-3 + file LICENSE
Depends R (>= 3.6)
Imports GenomicFeatures, tximport, Biostrings, rtracklayer, biomaRt, jsonlite, methods, dplyr, data.table, sjmisc, grDevices, graphics, stats, utils, rslurm, rhdf5
Suggests knitr, testthat, rmarkdown, AnnotationHub, httr
SystemRequirements kallisto
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BgeeCall_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64) BgeeCall_1.14.0.tgz
macOS Binary (arm64) BgeeCall_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: